Maier R M, Neckermann K, Igloi G L, Kössel H
Institut für Biologie III, Universität Freiburg, Germany.
J Mol Biol. 1995 Sep 1;251(5):614-28. doi: 10.1006/jmbi.1995.0460.
The nucleotide sequence of the chloroplast (cp) DNA from maize (Zea mays) has been completed. The circular double-stranded DNA, which consists of 140,387 base-pairs, contains a pair of inverted repeat regions (IRA and IRB) with 22,748 base-pairs each, which are separated by a small and a large single copy region (SSC and LSC) of 12,536 and 82,355 base-pairs, respectively. The gene content and the relative positions of a total of 104 genes (70 peptide-encoding genes, 30 tRNA genes and four rRNA genes) are identical with the chloroplast DNA of the closely related species rice (Oryza sativa). A detailed analysis of the two graminean plastomes allows the identification of hotspots of divergence which predominate in one region containing a cluster of tRNA genes and in two regions containing degenerated reading frames. One of these length differences is thought to reflect a gene transfer event from the plastome to the nucleus, which is followed by progressive degradation of the respective chloroplast gene resulting in gene fragments. The other divergent plastome region seems to be due to the complete loss of a plastid gene and its functional substitution by a nuclear encoded eukaryotic homologue. The rate of neutral nucleotide substitutions is significantly reduced for protein coding genes located in the inverted repeat regions. This indicates that the existence of inverted repeat regions confers increased genetic stability of the genes positioned in these regions as compared to genes located in the two single copy regions. Editing events cause the primary structures of several transcripts to deviate from the corresponding genomic sequences by C to U transitions. The unambiguous deduction of amino acid sequences from the nucleotide sequences of the corresponding genes is, therefore, not possible. A survey of the 25 editing positions identified in 13 different transcripts of the maize plastome shows that representatives of all protein coding gene classes are subject to editing. A strong bias exists for the second codon position and for certain codon transitions. Based on the number and the codon transition types, and taking into account the frequency of putative editing sites in all peptide encoding genes and unidentified reading frames, a total number of only few more than the experimentally verified 25 editing sites encoded in the maize plastome is estimated. This corresponds to 0.13% of amino acid positions which cannot be derived from the corresponding codons present in the corresponding genes.
玉米（Zea mays）叶绿体（cp）DNA的核苷酸序列已测定完成。该环状双链DNA由140,387个碱基对组成，包含一对反向重复区域（IRA和IRB），各有22,748个碱基对，它们被分别为12,536个碱基对的小单拷贝区域（SSC）和82,355个碱基对的大单拷贝区域（LSC）隔开。总共104个基因（70个编码肽的基因、30个tRNA基因和4个rRNA基因）的基因含量和相对位置与近缘物种水稻（Oryza sativa）的叶绿体DNA相同。对这两个禾本科植物叶绿体基因组的详细分析使得能够鉴定出分歧热点，这些热点主要存在于一个包含tRNA基因簇的区域以及两个包含退化阅读框的区域。这些长度差异之一被认为反映了从叶绿体基因组到细胞核的基因转移事件，随后相应的叶绿体基因逐渐降解，产生基因片段。另一个叶绿体基因组分歧区域似乎是由于一个质体基因的完全丧失及其被一个核编码的真核同源物功能替代所致。位于反向重复区域的蛋白质编码基因的中性核苷酸替换率显著降低。这表明与位于两个单拷贝区域的基因相比，反向重复区域的存在赋予了位于这些区域的基因更高的遗传稳定性。编辑事件导致几个转录本的一级结构通过C到U的转变偏离相应的基因组序列。因此，从相应基因的核苷酸序列明确推导氨基酸序列是不可能的。对玉米叶绿体基因组13种不同转录本中鉴定出的25个编辑位点的调查表明，所有蛋白质编码基因类别的代表都受到编辑。第二密码子位置和某些密码子转变存在强烈偏向。基于密码子转变类型的数量，并考虑到所有编码肽的基因和未鉴定阅读框中推定编辑位点的频率，估计玉米叶绿体基因组中编码的编辑位点总数仅比实验验证的25个编辑位点多几个。这相当于0.13%的氨基酸位置无法从相应基因中的相应密码子推导得出。
